Operation DNA
by Fluffeh turtle
Summary: Amy is captured by Shadow and saved by Sonic. What happens when she swithches from good to bad? Will Eggman and Shadow finally win with Amy on their side? and what is Operation DNA? Read and find out./Shadamy\\
1. Shadow's little helper

"Are you ready?" Shadow asked a tied and gagged Amy. She nodded, he grabbed her bridal-style and took her out on a balcony. The two were in a old abandoned warehouse that Shadow had made into his 'lair'.

Soon there was a hole in the roof and four people entered Sonic, Sally, Tails, and Viper. "GIVE HER BACK SHADOW!" Sonic 's voice echoed in the empty building. "You want her? Come get her hedgehog!" Shadow yelled. Sonic jumped on the balcony and ran to Shadow intending to punch him, but Shadow grabbed his fist and slammed Sonic on the ground.

Sonic got up and quickly jumped off the balcony down to the other three. Shadow was about to jump too but amy saw the look he had, So she swiftly swung her left leg until her heel made contact with shadows knee.

"OW! What the hell Rose?" Shadow yell/whispered at her she shook her head as if to say 'Don't kill them. We need them alive for the plan.' and Shadow understood her and nodded. "YOU WANT HER THEN HERE!" Shadow tossed Amy off the balcony. She was caught by Sonic "What game are you playing here Shadow?" sally asked.

Shadow shook his head. "You got Rose, now...**GET OUT!**"

_**AMY~**_

Once we got back to knothole Viper cut my ropes with her claws and I ripped off my gag off. Luckily only Sally noticed my change in clothes.

Instead of my childish red dress and boots I now wore a black crop top, a black backpack, a black frilly short skirt, and knee-high black latex boots. I quickly walked to the villages main lab with Tails and Sally close behind.

To be honest it was nice to be back. Shadow had 'kidnapped' me a week ago, not sure I consider it kidnapping any more. I bet they just figured out I was missing today. It sure wouldn't surprise me.

Once inside the lab I take quick notice to the fact that absolutly no one was here. I twirl around to face tails. "Where is everyone?" I asked him. "Everyone's out looking for you, which reminds me we better tell everyone we found you." He told me as he went to the main computer.

I quickly push tails away from the keyboard causing him to land on the ground while Sonic, Sally, and Viper all stare at me. "WHAT THE HECK AMY?" Tails screamed towards me. I felt a creepy and dark smile form on my face, "Sorry old friends." I whispered, I drop and do a hand stand and fling my legs around in a circle knocking all four of them out.

_**VIPER~**_

I woke up with a start. I look around me and see Sonic, Sal, and Tails all asleep. Then I notice we're in the knothole's main lab. Across from me outside the glass is Amy sending a message from us.

'no luck findin ames yet lets look ovr nite for her, k' Amy was using Sonic's text slang and nickname for her to make it convincing. Once she was done she directed her attention to us. "ah, Viper I see your awake. How did you sleep?" she asked in a cold and harsh tone.

"WHY ARE YOU DOING THIS!" I screamed at her now noticing her scary look. Her eyes half closed a demonic smirk on her face hands on her hips, this wasn't normal Amy at all. "That is classified." she said in the same harsh tone as before.

She walked a few feet away and took of her backpack, That I just noticed, and pulled out a dark purple cell phone. She dailed somebody's number and held the phone up to her ear. "Hello?" a equally harsh voice awnsered. I know I've heard that voice before... who is it?

"Hey I'm ready for you to come here" she told him. "Good job Rose I'll be right over." he said and hung up. At that she snapped her phone shut and looked back at our glass cage. I turn around and see that Sally and Sonic were awake. "Was that Shadow? Amy what are you doing with Shadow?" Sally asked just as confused as me. "Classified information Sally."

"-**CONTROL!**" Screamed Shadow as he put his chaos emerald down. He opens his eyes and glares at us, Then walks towards Amy. "Okay I've never been here before so, where is the Data central computer?" Amy walked in the direction of the computer.

She kept walking until she was at the biggest computer in the lab and stopped. "This computer should have all the information we need." he nodded and gestured for her to go on. She threw us a evil smirk and started typing. I heard Sally gasp, "I-I tried to teach Amy about the technology in here but she said she didn't get it!" sonic nodded "yeah she kept coming to me asking what each computer did!" he said.

"So Amy has been faking the whole time?" I asked "no..." Amy replied. "At the time I really didn't get this stuff... But Shaddie here helped me out." hearing her talk so sweetly of the enemy made me cringe. Shadow also seemed...embarassed by the use of the name Shaddie.

Woah, Shadow showed emotion. "GOT IT!" Amy cried happily. Shadow redirected his attention to the computer as Amy opened a file. I had never seen the file but apperently she had. I had to squint a little but I was able to read 'DNA FORMULA' at the top. "Great, Eggie should be pleased." Shadow told her as she printed the file out. Then she typed a special lock code so no one else could see it but her. 


	2. Coffee Shop

**HOLA! heh sorry for taking sooo long I've been trying to download a Rom -_-' it's very frustrating. ok last time I forgot to add a disclamer. oops ^_^' so... Sonic and all related characters belong to SEGA. Now on to the story._**

Shadow and Amy slowly made their way down a metal coridor inside Eggmans secret underground base. The base was lined with security camaras and purple robots, None of the robots even paid attention to the two as they walked toward a door that led to Eggman himself.

Once they walked through the door they saw Eggman typing at his computer looking quite frustrated. "Hello?" Amy called toward the fat man in red. Eggman spun around in his chair and eyed the two hedgies before him.

"Shadow what is she doing here?" he said pointing toward Amy. "I'm working for you now..." she told him "Besides she got you a present." shadow mumbled as Amy walked up to Eggman file in hand. "Here..." she growled and threw the file at him

"GAH" he screamed as he flipped over in his chair from the file hitting him in the face. Amy snickered at his expression and walked back to Shadow's side. "What is this?" Eggman asked the two gothic-like hedgehogs

"I call it Operation DNA. The plan is to create your own minions but instead of metal ones you can make actual living beings." a look of surprise formed on Eggmans face as Amy discribed the plan.

"Sure you could make a DNA model but this will alow you to create a being as a baby or adult, any and every detail can be made and changed by the creator... you." a evil smirk formed on her face as she spoke.

_**Shadow**_

Once Amy had explained the plan to Eggman he ran over to his work station covered with blue prints and rusted robots. With a quick swipe all the supplies fell to the floor as he spread the file on the table.

He looked from one page to the other taking in the information. "I had never thought of this! This could work." He yelled. Amy came over to me and kissed my cheek. I knew I was blushing I felt my cheeks getting hot.

I look back at Eggman to see him typing on his computer until he noticed we were watching him. "_**leave.**_" he told us. Amy grabbed my hand and walked off muttering something like "Ungreatful Little..."

After we got outside The base Amy suggested we go to the city and find a place to stay. "But Rose we have a place." I explained. She shook her head. "No we don't. I will not live in a warehouse or a Underground Pit." She nearly screamed at me. knowing her VERY short temper I took her to the city...

_**Amy**_

Shaddie and I were walking on the sidewalk in Station Square. **(**_**A/N ok I know knothole and station square are diffrent universes but for this story they both exist here.)**_ looking for a open appartment. Honestly I wouldn't mind the Old Warehouse as long as we lived together, Pretty corny right? Meh.

As we were walking I saw something Blue and Orange. It couldn't be...Could it? Yep it was, Sonic The Hedgehog and Tails coming right toward us. Shaddie hadn't seen them yet so I started to tug on his arm toward a coffee shop. "Huh? Oh A coffee shop, Alright." he said before I litterally dragged him in the shop...

"Okay..." he said while dusting himself off. Did I mention Shaddies a bit of a clean freak. I pulled shaddie toward a table in the far back, away from any windows. Once seated I peer out the window as Sonic, Tails, and the unnoticed-till-now Cream walk by.

Cream's eyes were glassy as if about to cry. Tails who had a bruise on the head thanks to my shoe, was looking downwards saying "I Don't belive it..." shaking his head. Sonic also wore a bruise on his head, He was patting Tails' back his eyes a bit glassy themselves.

_**Cream**_

Tails and were explaining what happened the other day with Amy. I thought we were best friends...I guess I was wrong. Tails said she was acting a little weird at first. Then he saw her outfit change. Then he said she knocked him down and kicked them all in the side of the head.

That _would_ explain why Viper has a bruise on her head and refuses to talk. Amy, Viper, and I were really close and- Wait was that sobbing? I turn my head to Tails and see him crying muttering something under his breath.

I felt my own tears starting to form. How could she do this to us? I mean the cheerful, energetic, happy, Sonic-loving, pink girl turned bad? How weird that is I mean even asivap is still on our his weird-o name...

**(A/N asivap is a random guy I made up he has no importance and might never appear again unless as an extra he is a sinister looking turtle.)** I look around to see if I can find anything of intrest. But it seemed that the city was dull since no activity of intrest could be found.

I decide just to look to the sky. It was grey lined with clouds the sky completley matched my emotions right now. Then I see something out of the corner of my eyes something pink...

**So what didja think? Good, Bad, Banana? you choose (sorry its a weird thing me and my friends do.) also wish me luck I think the rom is working YAY ^w^. Okay See You Later! **

**P.s. sorry its so short...**


	3. RoofTop Drop

**HI! I'm Fluffy and this is the ever so happy SHADOW!**

**Shadow:hi...**

**See what I mean? Anyway lets let shadow here do the disclaimer!**

**Shadow:Why Me!**

**Do you want to remain a Male in the story?**

**Shadow:Fluffy does not own me Amy, Sonic, Cream, Tails or anyone else possibly mentioned. Names you do not recognize probley belong to Fluffy. Happy?**

**Nope but lets get on with the story!**

_**Amy's POV**_

Shadow and I decided to travle back to the forest roof top style. We went on about three roof tops before I slipped on the edge of the building. Shadow reached for me but was to late I was falling. I squeeze my eyes close waiting for the impact, The painful crunch of my back or neck. but it never came. I slowly open one eye to see why I didn't hit. When I opened my eye I saw a pair of ruby eyes staring at me. Was I daydreaming? "You okay?" he asked me. I nearly sighed at his velvety voice. "Yeah just a daydream." I told him. He nodded and stood up.

"Ready to go?" He asked. "yeah..." I mumbled. That dream felt SO real like when your asleep and have a dream but don't realize its a dream until you wake up thats what I felt. Once shaddie and I were outside he looked at me. "want to go on the roof tops?" he asked me. I instantly shook my head 'no'. "Too bad..." He whispered and grabbed my wrist. He jumped to the building closest to us and then a higher building and another. He did this until we had made it to the tallest building in mobius. He stood at the top as I dangled of the side. He gave me a evil smirk and thats when I knew. This **WASN'T** shadow. "Bye..." he muttered and then dropped me.

_**Shadow's POV**_

I patiently stared at my bed and its occupant. On my bed knocked out and posibly hurt sat Amy Rose. She was in good condition thanks to the beige rabbit that caught her when she fell. I didn't suspect anything of the beige rabbit so I went down to her and attempted to get Amy. Turns out she was friends with 2-tail and faker. I asked of them to just peacfuly hand her over. They of course didn't want to. The rabbit seemed very close to Amy. They had decided that they wanted to run some _tests _on her so I had to grab her and run, and when I say run I mean **RUN**. Stupid Sonic was on my tail the entire time. He is so annoying...-**BANG**- What was that? I walk over to the door of my warehouse only to find a huge dent in the diamond-steel door. What? I needed a strong door. Another loud bang sounded in the warehouse.

I look over at Rose to find she was awake. Those stupid noises must have woken her up. She turned and looked at me and started screaming a horrible bloody murder type scream.

_**Normal POV**_

Once Amy woke up she took in her surroundings. 'Heaven? No. Hell? Maybe. Shadow's Warehouse? Crap.' Just to make sure, the pink and black girl turned around and sure enough met the eyes of Shadow The Hedgehog. All she thought to do was scream. Scream and scream until someone saved her. Shadow quickly sped up to her side and covered her mouth. "Shhh... Please Rose it's me Shadow. Remember?" He whispered to her. Amy thought for a moment. Had what happened been real? She examined her self. She didn't have any bruises or scratches except on her leg where a large scrape was placed seemingly glaring at her. From what she remembered Shadow dangled her over the edge of a tall building. She never hurt her leg and from the force Shadow was holding her wrist it should have a bruise.

'It was just a dream?' Amy thought to herself before she heard another loud bang go off "WAA IIIS HAA SHADA!" Amy attempted to ask but the task seemed rather difficult with Shadow's hand over her mouth. "Sorry. Now what did you say?" Shadow asked once he removed his hand. "What is that Shadow?" She asked. He looked at the dented door and mouthed the words 'lunatics.' That made her giggle a bit. "It's probably Faker, Two Tail, and Bunny." He muttered. "WHAT! Why are Sonic, Tails, and Cream Here? WHAT DID YOU DO!" She screached. He shook his head. Yet another bang was heard. 'We got to GO!' Shadow's thoughts screamed at him. He grabbed Amy and Choas Controlled away as soon as the door gave way and Freedom Fighters filled the warehouse.

Shadow and Amy arrived at Eggman's Base only to find him nearly crying. "Eggman whats the matter?" Amy asked roughly but sweetly. He turned to the newly noticed hedgies and smiled, not smirked or grinned but a happy relived smile. It scared both the hedgehogs to death but they stood still. "Listen. You two are going to help me make my own army. OK? I need a section of hand to hand fighters a speed section maybe even a tech section. Sharp shooters, Nurses, any special skill that you feel will help." He nodded and walked off leaving Amy and Shadow infrount of two data computers. They were specialy designed for writing DNA code. Amy went right to work and soon after Shadow joined.

**Three Days Later~**

"EGGMAN! WERE DONE!" Amy yelled down another dark corridor. Shadow and Amy had finished creating the perfect Egg-Army but they had no luck finding Eggman. "ATTENTION ALL WORKERS ARE TO REPORT TO THE MAIN LAB THIS INSTANT FOR EGGMAN TO PICK SQUAD LEADERS. THAT IS ALL." A cold metalic voice called from the intercom. Shadow and Amy turned around and ran for the main lab where Eggman was creating his perfect army.

Once the two arrived at the main lab they saw every mobian they specialy designed. The group was a varity of foxes, hedgehogs, dogs, cats, lizards, You name it you could find it. All of the souldiers were in their best years, 20-25. "Agility Squad!" Eggman called out to the large group. 50 of the 1000's walked over to him and were dressed in light blue combat suits. After Eggman was done sorting he had a bunch of colored groups like: Light Blue, Black and Red, Pink, Orange, Tan, Brown, Teal, Lavender, Yellow, Green, Gray, and more.

Eventually Eggman stood up and called their attention. "Welcome my beautiful army. Now I shall inform you who we will attack first! Our first victums will be..."

**Cliffy~ **

**Maybe... Anyways Thank You For Reading Chapter 3 Of Operation DNA. Next Chapter We May See Eggman Going Bonkers. So Nothing New. Oh! Sorry About The Long Wait My English Teacher Thinks It's Funny To Give Out 5 Projects The Same Week As The Science Fair. I Also Plan To Get The Next Chapter Up Sooner Now That I'm Done With All Those Projects. So Ta-Ta For Now.**

**Fluffy signing out~**


	4. Rat Attack

**^w^ Hello! Fluffy Reporting In! To My Loyal Readers I Say Gracias! That Is The Only Spanish Word I Know Besides Hola and Gato. Any Way I Do NOT Own Any Sonic Characters At All OR The song lyrics below they belong to Magna-Fi. Thank you and lets begin. **

"-Squad brown!" Eggman finished. Squad Brown stepped out of the crowd, the team was made of a purple lion at the age of 15, a 6 year old hedgehog, and a few other young mobians. Amy had been confused when she was told to make a few young ones and cripples. All the mobians like that were put in squad brown. Their sybol was some one getting punched, Shadow and Amy had thought the sybol ment that they were the strengh team. Turns out that they are the punching bag team.

Hours later. Amy

Well the brown squad doesn't exist any more, that's just great. After watching all the teams kill the teens and children of brown squad Shadow and I decided to leave to see what damage became of the warehouse. Once we got there the first thing we noticed was well... The giant whole where there used to be a door. Once we entered we found that all of our stuff had been trashed. When we went back to the hideout eggman already knew about the warehouse and gave us a room here. **A **ROOM. Shadow's nice and all but he's to neat freaky. I like organized chaos more. But Shadow says there's no such thing.

Well that brings us to now. Shadow is running around sweeping and cleaning the dust pit as he calls it. Me? I'm sitting on the top bunk-bed listening to my ipod app IHeartRadio. Right now the song is No One Knows by Queens Of The Stone Age. It's not that great. So I pull out my earbuds till the next song. As entertainment I watch Shadow run around the room smashing the broom on the white tiled floor attempting to kill a rat.

Somehow the rat's winning. Everytime Shadow gets close to it it runs in the hole infested walls. Quickly becoming bored I stick my earbuds back in to hear a familiar song.

_All hail Shadow_

_Heroes rise agin_

_Oblitering everything thats not your friend_

_Nothing can stop you now, _

_No ghost to bring you down_

_When there's nothing left to lose _

_You win~_

I begin to hum to the music while still watching shadow trying to 'Obliterate' the rat. I swear if he ever sees another rat after this his brain will snap. I decide to lay back and enjoy the rest of the song until I hear a loud THUD. With my earbuds still in I look up to see Shadows head in one of the rat holes. I'm not going to question the stupidity, just fix it. I grab Shadows legs and pull as hard as I can. Of course since I still had my ear buds in I couldn't hear any agonizing screams.

I gave one last hard tug and his big spikey head popped out of the tiny crack that hadn't gotten any bigger. Again don't question things around Shadow you will only be more confused. After giving his head a slap I crawled back on my bed. But out of the corner of my eye I see a black and red hedgehog smash a broom to the ground and run. I feel bad for Shadow and the Rat.

MEANWHILE with Viper and Cream

The two girl are taking a pleasent stroll through the woods enjoying the sound of nature."I'm seriously worried about Amy, Cream." Viper told the young rabbit. "Me too we all think Shadow kidnapped her and brainwashed her." Cream mentioned. Viper thought about this 'Could he do that? Why would he use Amy? I have sharp claws, Sally Is the best fighter, Bunnie is super strong why not one of us?' All these thought and more ran through her mind. Cream came up with similar thoughts earlier. Why Shadow picked Amy is an enigma to them but he must have his reasons. The two continued to walk in silence until they reached knothole and went their seperate ways.

Back with Shadow and Amy/ SHADOW

I can't belive we agreed to this. To live in a completely white room. I mean white walls, white beds, and a white table are all that's in here. I can't belive Rose got to sleep. Especially with that loud music she's listening to. I can't tell but it sounds like Faint By Linkin Park. Good song but not very good at keeping the sleeping well... asleep. But she continues to snooze. I can't stop looking at her. She's captivating, beautiful, stunning, and well everything a guy could ever want in a girl.

How could Faker choose anyone over this girl. She dedicated her life and love to him, only to get hurt. Although he did seem rather angry and concerned for her. But she says he would be like that if it were any of his friends and probably alot worse if it was Sally. I'm not so sure but not going as far as calling Rose a liar. Crap! She's waking up! I swoop back under her bed to mine and pretend to sleep as she gets up for some coffee. Where did that come from? I never made her coffee. Meh, Stupid robots. Once she finished her coffee she came back to the ladder to get on her bed once she got up there I relaxed a little.

"Oh and Shaddie your a terrible actor." She giggled as she went back to sleep. Crap.

**OMG finished yay! Now I need you oppinion is it too short because if it is then I will continue to type this. If not then I'll start on the next chappie. Also I just have to say this I LOVE ALL HAIL SHADOW! *fangirl squeel* and I love youth of the nation. THANK THOSE TWO SONGS FOR THE COMPLETION OF THIS CHAPTER! All right well it's 4:00 AM and I can't sleep because I want to listen to a early morning talk show that comes on at five... DON'T YOU JUDGE ME.**

**Tah-Tah for now **

**Fluffy out~**


	5. Hooked up

**Okay Fluffy's back with another chapter of Operation DNA. To be honest I got so wrapped up in writing 'Free Again' I almost forgot about this story. ^^ oops? Anyway the only reason I remembered this story is cause my BBFF (bestest best friend forever) has been calling, texting, and nagging me about "Whens the next chapter up?" or "What happens next?" or "Are you writing the next chapter? Which chapter are you on? Can I ask for something to happen in the story?" she won't leave me alone so if she wasn't ALWAYS nagging me I would never get this story DONE so... Heh.**

_Eggman's POV_

"AMY,SHADOW GET IN HERE NOW!" I screamed throught the extra loud speaker I hid in their room. I kept the speaker on to here their reaction. Amy was snoring while shadow was mumbling swear words. 'How is she asleep?' I thought. "Shadow wake Amy up for me will you?" I asked into the speaker. I kept listening in at first I heard Shadow threaten to splash Amy with water then a loud 'thud' and a few swear words from Amy. THEN I hear a loud 'SMASH' and a girly scream that wasn't Amy's. 'Poor Shadow.' I thought.

Ten minutes later Amy and Shadow appear in front of me. "HI there you two having a nice day?" mockery and sarcasm obvious in my voice. "SHUT THE F*** UP." Amy said in a loud but dull tone. "Thats no language for a lady. Especially when that lady is speaking to her boss. Hmmm..." I said. She gave me a hateful glare and in fear of her hammer I decide to move on. 'No doubt in my mind that the loud smash I heard earlier was from that over sized mallet.' I thought.

I suddenly remembered why I called them here. "Oh yes! I have a mission for you two." I exclaimed. Amy's face didn't change. Shadow showed some curiousity. "What mission?" Shadow asked. I pulled out a note from my pocket and handed it to him. I found the note this morning at the warehouse It's from Sally Acorn." I told them.

Dear Shadow,

We continue to queston why you chose Amy to 'Brainwash' in stead of The best martal Arts fighter, me. Or the strongest, Bunnie Rabot. Or even Viper with her sharp claws. Anyway we the freedom Fightrs would like to talk to you and maybe Amy. I know you probably think this is a trap. It isn't but if you don't trust us then don't you decide to come meet me and a few others at the freedom fighters clearing at 3:00pm tomorrow.

,Love Princess Sally Acorn

"Should we go Shadow?" Amy asked him. I cleared my throught. "Your mission is to go to the freedom fighters base and see if it IS a trap. If it isn't then you will go unarmed." I explained. "-And if it is a trap?" Amy questioned. "I'll tell you later now GO" I told them and pointed towards the door. Shadow and Amy ran out of the base and into the forest where I couldn't see them. 'Have fun.'

_Amy's POV_

After we left the base Shadow and I went up in the trees. I'm still a little nervous about heights since that horrible dream but I'm slowly getting over it. We continued on our path for awhile until we saw the freedom fighters clearing. No one was there. So we kept moving until we saw the main village and base. Shadow and I started to look around for anything suspicious.

I saw Sally and Tails standing by the main lab. I moved to a tree closer to them. "So why arn't we going to attack Shadow and rescue Amy?" Tails whispered. "Because I want a civilized talk with them. If we attack Shadow or Amy we might not get any information." Sally reasoned. "I guess but what if they attack us? Or don't show up?" Tails countered. "Then we fight back or they just don't show. If they arn't there by 4 then we leave. Now I'm DONE." Sally explained and stomped away.

'I guess it isn't a trap...' I thought. I quietly went back to Shadow and told him we could go. He nodded and started tree-hopping back to the base. Once we were a safe distance away he asked why we left. "Cause I got the info we need. Tails wants to trap us but Sally told him it wasn't going to be a trap." I explained. He nodded and focused back on the trees.

Once we got back to the base and reported our findings to Eggman. "Very well I would like the two of you to go to this thing." he said holding up Sally's note. "-But take these." He held his hand out and in it was 2 red dots and two purple dots. he handed me the red dots and Shadow the purple ones. "These are teleporters. If something bad happends just think of a place and think 'go' and you will be teleported there." He explained. "The dots are adhesive so put them where you like." He told us and then went back to work. 'Cool! I'm wearing them as earings.' I thought and put the dots on my ears.

"Where'd you put yours Shadow?" I asked. He pointed to the base of his ear. "If someone sees them they'll think they're earings." He said. I nodded and smiled at him.

_Next Day at 2:55pm_

"Shadow we're early..." I mumbled. Shadow and I were sitting in the trees waiting for all of the freedom fighters to arive before we showed ourselves. Shadow sat in a neat and strict position while I sat in a more Sonic-like pose. After all I did have to wake up early. 'Stupid meeting... Why hold a meeting so early in the morning?' I questioned myself. I nearly dozed off when I heard talking in the distance. Shadow and I looked and saw Tails, Sally, Sonic, Cream, Viper, Bunnie, Knuckles, and Rouge enter the clearing. "So what do we do now Sal?" Rouge asked the bordom already filling her voice. "Wait for Shadow and/or Amy to show up." Sally replied.

Shadow and I exchanged glances and nodded. Shadow jumped down infront of them with me right after landing perfectly next to him. This caused Sally to jump,Sonic to fall of the rock he was on, Knuckles to widen his eyes, Viper didn't move, Cream screamed, as did Rouge. I slightly snickered at their foolishness. "Princess Sally, What is it you wish to speak to us about?" Shadow asked.

Sally regained her composure and spoke "As I asked in the note we wish to know why you chose Amy of all of us, to brainwash to help you." That made me mad. "1st: I didn't brainwash her. 2nd: I kidnapped Amy so Sonic would save her but one thing led to another and well..." Shadow trailed off. "Well what?" Sally urged him on. Shadow looked at me as if he wanted me to explain it. "You see we kind of... Hooked up?" I finished for him.

They all looked at us wide eyed and in horror. "Actually I'd say we're past hooking up and are... in love." Shadow explained. Sally looked as if she would pass out, Sonic's mouth hit the floor along with Knuckles' mouth, Viper looked flabbergasted, and Cream,Tails, and Rouge were gawking at us with looks of shock and again horror. They apperently couldn't wrap their heads around us being in love.

"H-How did this happen?" Sally asked nearly recovering from the shock. Shadow looked at me and I started the story.

_ Flashback_

_I was walking out of my hut to Cream's when someone came behind me and knocked me out. When I awoke I was sitting on a couch in a warehouse. I looked around but had no clue as to where I was. "What are you looking for, Rose?" Someone behind me said. I turn around to see Shadow standing there smirking at me. "Sonic's gunna go nuts when he hears you caught me!" I screamed at him. He gave me a questioning glace. "I don't understand you Rose. I hate to hurt you worse than faker does already but... why chase after someone you can't have, or someone who doesn't love you like you do him? Why not go after someone who does love you?" He asked me. I started to come back at him when I took his word into consideration. "I-I don't know..." I timidly whispered. "Because you don't like change Rose. That or you don't want to accept the truth." He said. "I'm scared to let go of Sonic because I know no one loves me and he is a hero to me so-" Shadow cut me off by kissing me. "Not true Rose. Not true." he whisped in my ear._

_End Flashback_

"-and thats what happened." I finished. They all looked at me with surprised faces, even more surprsed than when Shadow said we were in love. Sally tilted her head. "Thats all the shock we can take for today... Come on guys lets go back to the village." She said. She turned and looked at us. "Thank you for coming you two." I smiled and teleported back to the base with Shadow right after.

_Sally's POV_

'What the hell? Where did they go?' I thought to myself.

**Hi! Finally done with this chappie. Okay now after this I'm going to start writing 'Free Again' and may not update this story for a little bit. Don't worry I won't forget about this story. So Now you guys know how Shadow and Amy got together. Poor Sal shes confused as hell. If you don't understand anything then ask. And Shadow didn't drop Amy off of a building that was just a dream that Amy had. So You may all hug shadow without fear he will drop you off of a building.**

**~that's all. Fluffy OUT! PEACE**


	6. Eggman's Pains

_**Hiya guys! Miss me? I told you I wouldn't forget about this story. Okay so first of all I would like to thank everyone for reading and reviewing. When I see nice reviews it motivates me to write so here I am. -And like finally chapter 6 of Operation DNA I thought I would never get it done. So without further ado ~**_

_**Eggman: WAIT!**_

_**What?**_

_**Eggman: Because of this chapter... I hate you fluffy...**_

_**Oh... Okay! PARTY! Oh yeah also! I do not own any sonic or SEGA characters. Only the plot, Viper, and Eggman's suffering soul. :3**_

_**Eggman: She scares me...**_

_Normal POV_

Inside a thick metal bomb-shell like place a fat eggman sits. He awaits his little minions back from a misson he hopes is succsessful. He sits on his small chair with high threat of it breaking under his weight. 'What is taking so long?' The Eggman thought. Just that moment the two in question appear infront of him making him scream and reel back. From such a huge weight change Eggmans poor little chair snaps and he falls back and hits his head on the wall.

The pink and black minons look over at him and see that the 'good' doctor is knocked out. The two stare at him for a moment. "I blame you." The pink one said. Her black counter-part replies with a simple glare.

In a far off place from the Eggman and his two minons sits a two-tailed orange fox. The fox sits and looks into his handheld device. On the screen of the mini computer is infact the large egg-shaped man and the hedgehogs who aid him. "Hey Tails! What'cha lookin' at?" A femine voice asks. Tails turns to find his friend and leader Sally. "Oh hey Sal... Just looking in on our 'friends'" He told her.

Sally looked on the screen to see Amy and Shadow, The minons, Drawing on Eggmans face do to his accident. "What the?" She began. Tails shrugged "Just because they work for evil doesn't mean that they have no fun or sence of humor." Tails tells her. She gives him a half-nod and looks on the screen again.

Shadow wasn't on the screen and Amy was duct taping Eggman to the wall by his arms and legs. Shadow comes back into the screen area and has a peice of paper and a roll of tape. He pulls off a peice and puts it and the note on Eggmans forehead so they could see it. "How's he going to read it?" Amy asks him. Shadow thinks for a moment before flipping the note over so Eggman can read it when he opens his eyes.

"Well that was weird..." Sally said. Tails nodded and turned the hand held off. "Here you can take Nicole back now." He said and hands her the mini computer. "If you want to watch them go ahead but I have a date with Cream, so... later." Tails says to her. He then casually walks out of the lab. Sally looks at the computer "Nicole" and puts her away. "I'll check up on them later." She says to herself and walks out of the lab and into her hut.

_Amy's POV_

Shadow and I sat in our room watching a telivision that Shadow 'found'. We sat there until we heard Eggman scream and swear at us. I shrugged and Shadow chuckled. I hopped down from my bunk and Shadow stood up. We left our room and went to Eggmans little area. "Hey boss!" I said once we entered. "AMY! GET THIS TAPE OFF OF ME NOW!" He screamed. He hadn't been able to remove the note and couldn't tell Shadow was with me.

"My oh my what happened here?" I asked him. "DON'T ACT INNOCENT! AMY!" He screamed. I shook my head. "That's no way to speak to a lady doctor." I said. His blood was boiling. "I know... BUT YOU ARE NO LADY!" He yelled. I shrugged. I walked up to him and removed the note from his face. "Finally! Now you! I um... eep..." He replied. He looked at me in terror.

I had taken the liberty to bring out my hammer. "Excuse me sir but all complaints shall be handled by Piko here." I said. "Y-You are forgiven...?" He stuttered out. I nodded and pulled off all of the tape. "Your welcome~" I cooed and skipped to the room. "She scares me too..." Eggman whispered to himself. I sat in the room until Shadow came in. "What happened to you?" I asked. "Eggy finally noticed me and yelled at me for letting you taunt him." Shadow said and layed on his bed. "Oh. Okay." I said and watched the TV.

I sat up and flipped through the chanells until I found something intresting. "We need to get her BACK!" The woman on the TV screamed at a large crowd. The woman was Sally... She and the Freedom Fighters had called a meeting and were going to try to steal her away. _'Crap!' _my mind screamed. '_They can't take me away! Can they...? NO! Think Amy Think!' _

I started to freak out. The next thing I know I'm in Shadows arms. "Are you okay?" he asked. I shook my head 'no'. He held me close. "What is it? A nightmare?" He questoned me. "I wish..." I mumbled. "I found a thing... On TV it was a freedom fighter meeting. They're going to take me away..." I cried. He stroked the back of my head. "It's okay Rose. I won't let them take you away." He told me. "Really?" I asked.

He nodded. I threw my arms around his neck and kissed him. He kissed back. He nibbled my bottom lip begging for entry. I granted him entry. We stayed like that for severy minutes until the need for air was great. We broke apart and just sat in a tight embrace. "Can you sleep with me tonight? Not like that! But... You know..." I tried. He snickered. "Sure Amy..." He said. I was frozen for a moment. He hardly ever calls me Amy. I layed down next to him. I put my head on his chest and he wrapped his arms around me.

I was out in a matter of seconds. The next morning I woke up and I was still in Shadow's arms. "Morning." Shadow whispered. I purred and snuggled closer to Shadow's chest fur. "Shadow and Amy if the both of you could please come to my office." Eggmans voice boomed through the loud speaker. Shadow began to get up but I pulled him back down. "We don't HAVE to Shadow. Just lay back down and relax." I told him. He thought about it for a moment. He eventually just layed back down.

"Thanks Shadow~" I cooed. We layed there in eachothers arms for what felt like hours. Until we heard someone knock on the door. We ignored it. Then the door opened and in stepped Eggman. "Whoa, Whoa! I gave you two seperate beds for a reason! Arn't you guys to young for that?" Eggman asked. I grabbed my hammer and threw it at his head. He screamed like a little girl and was K. .

"Nice." Shadow said. I giggled 'Poor Eggy having to deal with us.' I thought. Shadow went on to Eggman's "Office" and I got dressed. While I was getting dressed Eggman woke up and was looking at me. So I hit him with my hammer. Again. Then ran off to the office with Shadow. A little later Eggman finally walked in. "Look who decided to wake up." Shadow said. I shook my head in disappointment. "YOU TWO ARE GOING TO BE THE DEATH OF ME!" He cried. We just sat in our chairs looking nice and cute and innocent. "Anyway I called you here for your next mission."

_**The End~ of this Chapter.I swear this is like my most lovey dovey chapter of anything so far and... I LOVE IT! Finally an actual kiss for Shadow and Amy. So... What is Shadow and Amy's next mission? Will the freedom fighters attack or capture Amy? Can Shadow help? Will Amy finally kill Eggman with everything she does? Find out next Chapter.**_

_**Eggman: It's obvious why I hate you.**_

_**I know**_

_**Eggman: Why are you so okay about it?**_

_**Because I have the power to burn you.**_

_**Eggman: No you- AHHHHHHHHHHHHH!**_

_**Bye-Bye everyone Fluffy OUT~ PEACE**_


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